Tag: Map

PDB-Explorer – Web-based interactive Map of PDB in Shape Space

PDB-Explorer

:: DESCRIPTION

PDB-Explorer is a web application for the interactive visualization of chemical space of RCSB Protein Data Bank (PDB) characterized by protein shape fingerprint (3DP) and shape similarity search for molecules in PDB.

::DEVELOPER

PDB-Explorer team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PDB-Explorer: a web-based interactive map of the protein data bank in shape space.
Jin X, Awale M, Zasso M, Kostro D, Patiny L, Reymond JL.
BMC Bioinformatics. 2015 Oct 23;16(1):339.

elPrep 5.0.2 – High-Performance Preparation of Sequence Alignment/Map Files for Variant Calling

elPrep 5.0.2

:: DESCRIPTION

elPrep is a high-performance tool for preparing .sam/.bam/.cram files for variant calling in sequencing pipelines.It can be used as a drop-in replacement for SAMtools/Picard, and was extensively tested with different pipelines for variant analysis with GATK.

::DEVELOPER

The Exascience Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 elPrep

:: MORE INFORMATION

Citation

PLoS One. 2015 Jul 16;10(7):e0132868. doi: 10.1371/journal.pone.0132868. eCollection 2015.
elPrep: High-Performance Preparation of Sequence Alignment/Map Files for Variant Calling.
Herzeel C, Costanza P, Decap D, Fostier J, Reumers J

MethylViewer 20120328 – Interactive data analysis of Bisulphite DNA Sequencing to Map Chromatin Structure using DNA Methyltransferases

MethylViewer 20120328

:: DESCRIPTION

MethylViewer was developed from CpGviewer such that the program can now analyse up to four different methylation sites such as CpG, GpC, CpNpG or any four user defined sites. If a non-native DNA methylase is used to modify chromatin-bound DNA, the methylation pattern can be used to identify the binding sites of DNA-binding proteins.

::DEVELOPER

Ian’s DNA@Leeds

:: SCREENSHOTS

MethylViewer

:: REQUIREMENTS

  • Windows
  • Microsoft .NET framework version 2.0 

:: DOWNLOAD

 MethylViewer

:: MORE INFORMATION

Citation

Pardo C, Carr IM, Hoffman C, Darst R, Markham AF, Bonthron DT, Kladde M
MethylViewer: computational analysis and editing for bisulphite sequencing and Methyltransferase Accessibility Protocol for Individual Templates (MAPit) projects.
Nucleic Acids Res. 2011 Jan 1;39(1):e5

CoMap 1.5.2 – Map Substitutions on a Phylogeny and Detect Coevolution

CoMap 1.5.2

:: DESCRIPTION

CoMap performs two kinds of tasks:

(Weighted) Probabilistic substitution mapping – Compute all (weighted) number of substitutions occurring on each branch of a tree, for each site of an alignment.
Co-evolution analysis – Using the substitution mapping, look for significantly groups of sites departing the null hypothesis of independence. Two kind of analyzes are provided: a pairwise analysis, presented in Dutheil et al. (2005), and a clustering analysis in Dutheil and Galtier (2007). In both cases, a parametric bootstrap approach is used to evaluate the significance of groups. Simulation results are written to separate files, a statistics software like R is required to look for the significance.

::DEVELOPER

Dr Julien Y. Dutheil

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Bio++

:: DOWNLOAD

CoMap

:: MORE INFORMATION

Cite the following article if you use the pairwise method:

Dutheil J, Pupko T, Jean-Marie A, Galtier N.
A model-based approach for detecting coevolving positions in a molecule.
Mol Biol Evol. 2005 Sep;22(9):1919-28.

Cite the following article if you use the clustering method:

Dutheil J, Galtier N.
Detecting groups of co-evolving positions in a molecule: a clustering approach.
BMC Evol Biol. 2007 Nov 30;7(1):242

Cite the following article if you use the candidate approach method:

Dutheil JY, Jossinet F, Westhof E.
Base pairing constraints drive structural epistasis in ribosomal RNA sequences.
Mol Biol Evol. 2010 Aug;27(8):1868-76

GenGIS 2.5.3 – Combine Digital Map data with Genomic Data

GenGIS 2.5.3

:: DESCRIPTION

GenGIS is a bioinformatics application that allows users to combine digital map data with information about biological sequences collected from the environment. GenGIS provides a 3D graphical interface in which the user can navigate and explore the data, as well as a Python interface that allows easy scripting of statistical analyses using the Rpy libraries.

::DEVELOPER

Beiko lab

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 GenGIS

:: MORE INFORMATION

Citation:

Parks DH, Porter M, Churcher S, Wang S, Blouin C, Whalley J, Brooks S and Beiko RG. 2009.
GenGIS: A geospatial information system for genomic data.
Genome Research, 19: 1896-1904

EM-SURFER – Navigating 3D Electron Microscopy Maps

EM-SURFER

:: DESCRIPTION

EM-SURFER is a web platform for real-time electron microscopy database search. It compares isosurface shape of a query EM map against maps in the latest EMDB.

::DEVELOPER

Kihara Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Navigating 3D electron microscopy maps with EM-SURFER.
Esquivel-Rodríguez J, Xiong Y, Han X, Guang S, Christoffer C, Kihara D.
BMC Bioinformatics. 2015 May 30;16:181. doi: 10.1186/s12859-015-0580-6.

MAPanalyzer – Analyzing Microtubule-associated Proteins

MAPanalyzer

:: DESCRIPTION

MAPanalyzer is a MAP (Microtubule-associated Proteins) analysis tool.

::DEVELOPER

Ziding Zhang’s Lab, China Agricultural University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

MAPanalyzer: a novel online tool for analyzing microtubule-associated proteins.
Zhou Y, Yang S, Mao T, Zhang Z.
Database (Oxford). 2015 Nov 13;2015. pii: bav108. doi: 10.1093/database/bav108.

xMAN 20060925 – MAp OligoNucleotides to Subject Genome

xMAN 20060925

:: DESCRIPTION

xMAN (extreme MApping of OligoNucleotides) is a simple and efficient method for the mapping of millions of query oligonucleotide fragments to the subject genome of any given length. xMAN is at least an order of magnitude faster than other popular existing tools.

::DEVELOPER

X. Shirley Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  xMAN

:: MORE INFORMATION

Citation:

Li W, Carroll JS, Brown M, Liu S.
xMAN: extreme MApping of OligoNucleotides.
BMC Genomics. 2008;9 Suppl 1:S20.

NextGenMap 0.5.5 – Map NGS Reads against a Reference Genome

NextGenMap 0.5.5

:: DESCRIPTION

NextGenMap/NGM (Next Generation Mapper)is a computer program to map NGS reads against a reference genome using CPUs or GPUs.

::DEVELOPER

 the Center of Integrative Bioinformatics Vienna (CIBIV) headed by Arndt von Haeseler.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 NextGenMap

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Nov 1;29(21):2790-1. doi: 10.1093/bioinformatics/btt468.
NextGenMap: fast and accurate read mapping in highly polymorphic genomes.
Sedlazeck FJ, Rescheneder P, von Haeseler A.

MAP 20121108 – A de novo Metagenomic Assembly program for Shotgun DNA reads

MAP 20121108

:: DESCRIPTION

MAP (Metagenomic Assembly program) is a de novo assembly approach and its implementation based on an improved Overlap/Layout/Consensus (OLC) strategy incorporated with several special algorithms.MAP uses the mate pair information, resulting in being more applicable to shotgun DNA reads (recommended as > 200 bp) currently widely-used in metagenome projects. Results of extensive tests on simulated data show that MAP can be superior to both Celera and Phrap for typical longer reads by Sanger sequencing, as well as has an evident advantage over Celera, Newbler, and the newest Genovo, for typical shorter reads by 454 sequencing.

::DEVELOPER

ZhuLab, Peking Uiniversity, Beijing

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

MAP

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Jun 1;28(11):1455-62. Epub 2012 Apr 11.
A de novo metagenomic assembly program for shotgun DNA reads.
Lai B, Ding R, Li Y, Duan L, Zhu H.